I am using Kraken2 for Taxonomic classification of the Microbiome from Anammox process in the wastewater plant, so I want to know if I can actually classify Class Brocadiia or it just show them as uncultured ? or can you mention any other way to do it?
Hello @Sawant_Bharat
It seems your question was missed – maybe I can still help?
The indexes in Galaxy hosted for the Kraken2 tool are the same as those available here.
This would be a good place to check the content of the individual databases. Did you already check to see if the Core_nt or GTDB database includes it? What happens if you try to annotate with one of those?
Then, I asked ChatGPT if it knows .. and it does not beyond stating that the RefSeq division itself doesn’t, or rather, it couldn’t confirm that. So – your question stumped the bot, too! 
It is suggesting that you construct your own index but I don’t think that is very practical.
Let us know how your tests runs work against the two DBs above and we can try to follow up to get this actually answered. Thanks! 